[Robast-commits] r828 - branches/robast-1.0/pkg/RobLoxBioC/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun May 3 18:21:35 CEST 2015
Author: stamats
Date: 2015-05-03 18:21:35 +0200 (Sun, 03 May 2015)
New Revision: 828
Modified:
branches/robast-1.0/pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save
Log:
update of Rout.save file
Modified: branches/robast-1.0/pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save
===================================================================
--- branches/robast-1.0/pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save 2015-05-03 16:03:31 UTC (rev 827)
+++ branches/robast-1.0/pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save 2015-05-03 16:21:35 UTC (rev 828)
@@ -1,7 +1,6 @@
-R Under development (unstable) (2013-02-06 r61845) -- "Unsuffered Consequences"
-Copyright (C) 2013 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R Under development (unstable) (2015-05-02 r68310) -- "Unsuffered Consequences"
+Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -22,52 +21,18 @@
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('RobLoxBioC')
-Loading required package: Biobase
-Loading required package: BiocGenerics
-Loading required package: parallel
-
-Attaching package: ‘BiocGenerics’
-
-The following objects are masked from ‘package:parallel’:
-
- clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
- clusterExport, clusterMap, parApply, parCapply, parLapply,
- parLapplyLB, parRapply, parSapply, parSapplyLB
-
-The following object is masked from ‘package:stats’:
-
- xtabs
-
-The following objects are masked from ‘package:base’:
-
- Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
- cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
- match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
- rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
- union, unique, unlist
-
-Welcome to Bioconductor
-
- Vignettes contain introductory material; view with
- 'browseVignettes()'. To cite Bioconductor, see
- 'citation("Biobase")', and for packages 'citation("pkgname")'.
-
-Loading required package: affy
-Loading required package: beadarray
-Loading required package: ggplot2
-Welcome to beadarray version 2.9.1
-beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
Loading required package: distr
Loading required package: startupmsg
-:startupmsg> Utilities for start-up messages (version 0.8)
+:startupmsg> Utilities for Start-Up Messages (version 0.9.1)
:startupmsg>
:startupmsg> For more information see ?"startupmsg",
:startupmsg> NEWS("startupmsg")
Loading required package: sfsmisc
Loading required package: SweaveListingUtils
-:SweaveListingUtils> Utilities for Sweave together with
-:SweaveListingUtils> TeX listings package (version 0.6)
+:SweaveListingUtils> Utilities for Sweave Together with
+:SweaveListingUtils> TeX 'listings' Package (version
+:SweaveListingUtils> 0.7)
:SweaveListingUtils>
:SweaveListingUtils> NOTE: Support for this package
:SweaveListingUtils> will stop soon.
@@ -95,12 +60,12 @@
Attaching package: ‘SweaveListingUtils’
-The following object is masked from ‘package:base’:
+The following objects are masked from ‘package:base’:
library, require
-:distr> Object oriented implementation of distributions (version
-:distr> 2.4)
+:distr> Object Oriented Implementation of Distributions (version
+:distr> 2.6)
:distr>
:distr> Attention: Arithmetics on distribution objects are
:distr> understood as operations on corresponding random variables
@@ -121,128 +86,54 @@
Attaching package: ‘distr’
-The following object is masked from ‘package:stats’:
+The following objects are masked from ‘package:stats’:
df, qqplot, sd
-Loading required package: RobLox
-Loading required package: lattice
-Loading required package: RColorBrewer
-Loading required package: distrMod
-Loading required package: distrEx
-:distrEx> Extensions of package distr (version 2.4)
-:distrEx>
-:distrEx> Note: Packages "e1071", "moments", "fBasics" should be
-:distrEx> attached /before/ package "distrEx". See
-:distrEx> distrExMASK().Note: Extreme value distribution
-:distrEx> functionality has been moved to
-:distrEx>
-:distrEx> package "RobExtremes". See distrExMOVED().
-:distrEx>
-:distrEx> For more information see ?"distrEx", NEWS("distrEx"), as
-:distrEx> well as
-:distrEx> http://distr.r-forge.r-project.org/
-:distrEx> Package "distrDoc" provides a vignette to this package
-:distrEx> as well as to several related packages; try
-:distrEx> vignette("distr").
+Loading required package: affy
+Loading required package: BiocGenerics
+Loading required package: parallel
+Attaching package: ‘BiocGenerics’
-Attaching package: ‘distrEx’
+The following objects are masked from ‘package:parallel’:
-The following object is masked from ‘package:stats’:
+ clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
+ clusterExport, clusterMap, parApply, parCapply, parLapply,
+ parLapplyLB, parRapply, parSapply, parSapplyLB
- IQR, mad, median, var
+The following objects are masked from ‘package:distr’:
-Loading required package: RandVar
-:RandVar> Implementation of random variables (version 0.9)
-:RandVar>
-:RandVar> For more information see ?"RandVar", NEWS("RandVar"), as
-:RandVar> well as
-:RandVar> http://robast.r-forge.r-project.org/
-:RandVar> This package also includes a vignette; try
-:RandVar> vignette("RandVar").
+ width, width<-
-Loading required package: MASS
-Loading required package: stats4
-:distrMod> Object oriented implementation of probability models
-:distrMod> (version 2.4)
-:distrMod>
-:distrMod> Some functions from pkg's 'base' and 'stats' are
-:distrMod> intentionally masked ---see distrModMASK().
-:distrMod>
-:distrMod> Note that global options are controlled by
-:distrMod> distrModoptions() ---c.f. ?"distrModoptions".
-:distrMod>
-:distrMod> For more information see ?"distrMod",
-:distrMod> NEWS("distrMod"), as well as
-:distrMod> http://distr.r-forge.r-project.org/
-:distrMod> There is a vignette to this package; try
-:distrMod> vignette("distrMod").
-:distrMod> Package "distrDoc" provides a vignette to the other
-:distrMod> distrXXX packages,
-:distrMod> as well as to several related packages; try
-:distrMod> vignette("distr").
-
-
-Attaching package: ‘distrMod’
-
-The following object is masked from ‘package:stats4’:
-
- confint
-
The following object is masked from ‘package:stats’:
- confint
+ xtabs
-The following object is masked from ‘package:base’:
+The following objects are masked from ‘package:base’:
- norm
+ Filter, Find, Map, Position, Reduce, anyDuplicated, append,
+ as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
+ eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
+ mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
+ rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
+ unique, unlist, unsplit
-Loading required package: RobAStBase
-Loading required package: rrcov
-Loading required package: robustbase
-Loading required package: pcaPP
-Loading required package: mvtnorm
-Scalable Robust Estimators with High Breakdown Point (version 1.3-02)
+Loading required package: Biobase
+Welcome to Bioconductor
-:RobAStBase> Robust Asymptotic Statistics (version 0.9)
-:RobAStBase>
-:RobAStBase> Some functions from pkg's 'stats' and 'graphics'
-:RobAStBase> are intentionally masked ---see RobAStBaseMASK().
-:RobAStBase>
-:RobAStBase> Note that global options are controlled by
-:RobAStBase> RobAStBaseoptions() ---c.f. ?"RobAStBaseoptions".
-:RobAStBase>
-:RobAStBase> For more information see ?"RobAStBase",
-:RobAStBase> NEWS("RobAStBase"), as well as
-:RobAStBase> http://robast.r-forge.r-project.org/
+ Vignettes contain introductory material; view with
+ 'browseVignettes()'. To cite Bioconductor, see
+ 'citation("Biobase")', and for packages 'citation("pkgname")'.
-
-Attaching package: ‘RobAStBase’
-
-The following object is masked from ‘package:graphics’:
-
- clip
-
>
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
-> base::assign(".ExTimings", "RobLoxBioC-Ex.timings", pos = 'CheckExEnv')
-> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
-> base::assign(".format_ptime",
-+ function(x) {
-+ if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
-+ if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
-+ format(x[1L:3L])
-+ },
-+ pos = 'CheckExEnv')
->
> cleanEx()
> nameEx("0RobLoxBioC-package")
> ### * 0RobLoxBioC-package
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RobLoxBioC-package
> ### Title: Infinitesimally robust estimators for preprocessing omics data
> ### Aliases: RobLoxBioC-package RobLoxBioC
@@ -254,23 +145,19 @@
>
>
>
->
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("0RobLoxBioC-package", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("KolmogorovMinDist")
> ### * KolmogorovMinDist
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: KolmogorovMinDist
> ### Title: Generic Function for Computing Minimum Kolmogorov Distance for
> ### Biological Data
> ### Aliases: KolmogorovMinDist KolmogorovMinDist-methods
> ### KolmogorovMinDist,matrix,Norm-method
> ### KolmogorovMinDist,AffyBatch,AbscontDistribution-method
-> ### KolmogorovMinDist,BeadLevelList,AbscontDistribution-method
+> ### KolmogorovMinDist,beadLevelData,AbscontDistribution-method
> ### Keywords: robust
>
> ### ** Examples
@@ -288,7 +175,7 @@
[1] 100 100
>
-> ## using Affymetrix-Data
+> ## using Affymetrix data
> data(SpikeIn)
> probes <- log2(pm(SpikeIn))
> (res <- KolmogorovMinDist(probes, Norm()))
@@ -302,50 +189,15 @@
> boxplot(res$dist)
>
-> ## Not run:
-> ##D ## "Not run" just because of computation time
-> ##D require(affydata)
-> ##D data(Dilution)
-> ##D res <- KolmogorovMinDist(Dilution[,1], Norm())
-> ##D summary(res$dist)
-> ##D boxplot(res$dist)
-> ##D plot(res$n, res$dist, pch = 20, main = "Kolmogorov distance vs. sample size",
-> ##D xlab = "sample size", ylab = "Kolmogorov distance",
-> ##D ylim = c(0, max(res$dist)))
-> ##D uni.n <- min(res$n):max(res$n)
-> ##D lines(uni.n, 1/(2*uni.n), col = "orange", lwd = 2)
-> ##D legend("topright", legend = "minimal possible distance", fill = "orange")
-> ## End(Not run)
>
-> ## using Illumina-Data
-> ## Not run:
-> ##D ## "Not run" just because of computation time
-> ##D data(BLData)
-> ##D res <- KolmogorovMinDist(BLData, Norm(), arrays = 1)
-> ##D res1 <- KolmogorovMinDist(BLData, log = TRUE, Norm(), arrays = 1)
-> ##D summary(cbind(res$dist, res1$dist))
-> ##D boxplot(list(res$dist, res1$dist), names = c("raw", "log-raw"))
-> ##D sort(unique(res1$n))
-> ##D plot(res1$n, res1$dist, pch = 20, main = "Kolmogorov distance vs. sample size",
-> ##D xlab = "sample size", ylab = "Kolmogorov distance",
-> ##D ylim = c(0, max(res1$dist)), xlim = c(min(res1$n), 56))
-> ##D uni.n <- min(res1$n):56
-> ##D lines(uni.n, 1/(2*uni.n), col = "orange", lwd = 2)
-> ##D legend("topright", legend = "minimal possible distance", fill = "orange")
-> ## End(Not run)
>
>
->
->
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("KolmogorovMinDist", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("SimStudies")
> ### * SimStudies
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SimStudies
> ### Title: Perform Monte-Carlo Study.
> ### Aliases: AffySimStudy IlluminaSimStudy
@@ -379,16 +231,12 @@
>
>
>
->
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("SimStudies", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("robloxbioc")
> ### * robloxbioc
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: robloxbioc
> ### Title: Generic Function for Preprocessing Biological Data
> ### Aliases: robloxbioc robloxbioc-methods robloxbioc,matrix-method
@@ -419,47 +267,14 @@
[1,] -0.02545634 1.042738
[2,] -0.16757528 1.004658
>
-> ## Don't run to reduce check time on CRAN
-> ## Not run:
-> ##D ## the function is designed for large scale problems
-> ##D X <- matrix(rnorm(50000*20, mean = 1), nrow = 50000)
-> ##D system.time(robloxbioc(X))
-> ##D
-> ##D ## using Affymetrix-Data
-> ##D ## confer example to generateExprVal.method.mas
-> ##D ## A more worked out example can be found in the scripts folder
-> ##D ## of the package.
-> ##D data(SpikeIn)
-> ##D probes <- pm(SpikeIn)
-> ##D mas <- generateExprVal.method.mas(probes)
-> ##D rl <- 2^robloxbioc(log2(t(probes)))
-> ##D concentrations <- as.numeric(colnames(SpikeIn))
-> ##D plot(concentrations, mas$exprs, log="xy", ylim=c(50,10000), type="b",
-> ##D ylab = "expression measures")
-> ##D points(concentrations, rl[,1], pch = 20, col="orange", type="b")
-> ##D legend("topleft", c("MAS", "roblox"), pch = c(1, 20))
-> ##D
-> ##D require(affydata)
-> ##D data(Dilution)
-> ##D eset <- robloxbioc(Dilution)
-> ##D ## Affymetrix scale normalization
-> ##D eset1 <- robloxbioc(Dilution, normalize = TRUE)
-> ##D ## "Not run" just because of computation time
-> ##D require(beadarrayExampleData)
-> ##D data(exampleBLData)
-> ##D res <- robloxbioc(exampleBLData, eps.upper = 0.5)
-> ##D res
-> ## End(Not run)
>
>
>
->
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("robloxbioc", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> ### * <FOOTER>
> ###
+> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 12.136 0.156 12.385 0 0
+Time elapsed: 4.889 0.08 4.966 0 0
> grDevices::dev.off()
pdf
2
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